Comments (17)
Can you try that your tree.nek
file put on itol(https://itol.embl.de/)
websites to re-root. After export again as a nwk
format, you code will work! I hope this approach can slove the problem.
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Hi Mike
My best guess would be a spelling error in your tree file. If you can't figure it out, feel free to email me with your combined_tree.txt and the tree.nwk files, I can try to investigate.
Kind regards
Milan
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Hi Mike
Thanks for your patience. A few other people reported similar problems. The reason is: Dtrios just kind of "looks over” the tree to find the arrangement of the trios, whereas Fbranch needs to do a full tree data-structure parsing. So the code is different, and the Fbranch code was less flexible about the format of the input. In your case it was the dashes "-" in the taxon names that caused the trouble.
I have made the parser more flexible, so I think it should work with your file and also for people who have blank spaces in the group names. I also added a check for duplicate entries in the trees. This is all in the latest version r38.
Milan
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Hi Milan,
I've got the same problem with the version 0.4 r38
Dsuite Fbranch tree.txt sets__tree.txt > fbranch.txt ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: (Outgroup,internalNode1X,internalNode5X);
But my tree is very simple: (Outgroup,((a,b),c),(((d,h),(e,f)),g));
Do you have any suggestions?
best,
Evgeniy
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I had a problem with full stops (periods) in my names as well. Replacing with underscores fixed the problem.
@siberianhigh Try putting the outgroup at the end?
(((a,b),c),(((d,h),(e,f)),g),Outgroup);
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Hi Milan,
I've got the same problem with the version 0.4 r38
Dsuite Fbranch all10qa11qv.nwk out_combined_tree.txt > all10pop_branch.txt
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
(((((((internalNode0X,(internalNode1X)),TBS),internalNode4X),JJL),DWX),internalNode13X),Outgroup);
Do you have any suggestions?
best,
frr
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It looks like the brackets around (internalNode1X) might be redundant. Try removing them?
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Thank you for your reply. I have successfully solved this problem.
…
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Hi, I met the same problems as you. Could you please tell me how to solve it? Thanks!
((((((internalNode0X)))),(internalNode1X,((NUB),((SIB))))),((FAL.00099760),((BEZ),((WAS,((EUR),((SAF),(EAF,(NAF))))),((SAS),(SC,(NC)))))))
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Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?
from dsuite.
Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?
that means your tree string was not correct. you can check carefully tree string.
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Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?that means your tree string was not correct. you can check carefully tree string.
I used the tree generated by FastTree just removing branch values.
from dsuite.
Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?that means your tree string was not correct. you can check carefully tree string.
I used the tree generated by FastTree just removing branch values.
So did I, but the tree string generated by FastTree always didn't work for branch. I conducted a NWK file by myself.
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Thank you so much for your reply.
I am confused how would you revise/edit tree.
my tree looks like this:
(Outgroup,(18pop,((15pop,(17pop,16pop)),(7pop,(6pop,(5pop,(4pop,(3pop,(1pop,2pop)))))),((11pop,(8pop,10pop),((12pop,9pop),(14pop,13pop)))))));
PS: I have also tried putting outgroup at the end
from dsuite.
Thank you so much for your reply.
I am confused how would you revise/edit tree. my tree looks like this:
(Outgroup,(18pop,((15pop,(17pop,16pop)),(7pop,(6pop,(5pop,(4pop,(3pop,(1pop,2pop)))))),((11pop,(8pop,10pop),((12pop,9pop),(14pop,13pop)))))));
PS: I have also tried putting outgroup at the end
your original tree was showed in below according to your tree string. But I think there was something wrong with it.
Here I reconstructed a tree string: (((((((((((1,2),3),4),5),6),7),((((9,12),(13,14)),(8,10)),11)),((16,17),15)),19),O). I am not sure if it can success in Franch.
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Thank you very much. I removed 19 and it worked.
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Related Issues (20)
- Dtrios error: Assertion `p_S3a >= 0' failed
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- Question about order of population set when running Dtrios HOT 1
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- Fbrach error: The tree string could not be parsed correctly!
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- Compilation error HOT 1
- compatible VCF format with pool sequencing data option HOT 2
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- Could Dinvestigate (fd, fdM, and df) identify the direction of gene introgression?
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